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From: amin_at_imtech.res.in
Date: Fri Jul 20 2012 - 08:53:47 CDT
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I was working on your suggestion of using same intervals for dcd and
restart.However I read this at NAMD Wiki.
Set restartFreq to a large multiple of dcdFreq. Writing a restart file uses 6
doubles per atom compared to only 3 floats per atom for a trajectory file.
Writing restarts infrequently reduces the amount of data sent to node 0 by 75%
and the amount written to disk by 80%.
Can someone please suggest something else to escape my overlapping frames problem?
Amin.
> You misunderstand how restartFreq works. There will never be more than two sets
> of restart files, one for the most recent output and one for the previous
> output.
>
> -----Original Message-----
> From: amin_at_imtech.res.in [mailto:amin_at_imtech.res.in]
> Sent: Friday, July 20, 2012 1:41 AM
> To: JC Gumbart
> Subject: Re: vmd-l: Joining DCD files with overlapping frames.
>
> Thanks. But my dcd frequency in 500 and a restart frequency of 500 will make a
> whole lot of files.So I have kept restart frequency to 50000. Do you suggest
> making restart frequency 500? even in that case can you please suggest a
> solution to my current problem?
>
>
> Amin.
>
>
>> If you set your dcdFreq to the same as your restartFreq, then there
>> should be no overlap.
>>
>> On Jul 19, 2012, at 9:53 PM, amin_at_imtech.res.in wrote:
>>
>>> Dear all,
>>> I have five dcd files from simulation runs started using restart
>>> files of the previous run. Now, because I kept getting 'periodic cell
>>> has become too small', so I restarted from the latest available
>>> restart files. So, each of my dcd file has some frames common with
>>> the previous one. I think I can chop the overlapping frames from the
>>> each of the dcd files and then join them using catdcd, but is there a better
>>> way of doing this?
>>>
>>> Regards.
>>> Amin.
>>>
>>> _____________________________________________________________________
>>> _ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
>>> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF
>>> CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN
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>>
>>
>>
>
>
> ______________________________________________________________________
> सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of
> Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़
> / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665
> 201-202
>
______________________________________________________________________
सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद)
Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh
पिन कोड/PIN CODE :160036
दूरभाष/EPABX :0172 6665 201-202
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